Hi Daniel
Personally, I have never used the standard space masking function. I
have also been using MPRAGE 1mm iso images from a Trio scanner. We
collect our images saggittally which can lead to a bias field in the
temporal lobes if you don't collect enough slices. i recommend first
removing the neck using 'fslroi', then performing BET with the -S and -B
options. if you are using SIENAX you may still need to manually remove
some of the extra stuff around the pons or skull. if you are using SIENA
this should not be such a problem because the software looks at the
movement of the brain surface which is relative.
cheers
Scott
Daniel Reich wrote:
> Thank you. Looking at the images, my sense is that BET is working properly
> but that the standard-space mask is eating away at the cortex. Could this be
> because of the relatively low signal intensity of cortex on MPRAGE (i.e. too
> similar to CSF)?
>
--
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Scott Kolbe
MS Imaging Group
Howard Florey Institute &
Centre for Neuroscience
University of Melbourne
VIC, Australia, 3010.
ph: +61 3 8344 1887
email: [log in to unmask]
website: www.neuroimaging.org.au/index.php?id=383
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